Giorgio,
It is possible that the promoter has no TATA box. For example, look at the
Initiator element (eg the TdT gene). Also, I have come across TATA-less
promoters in some p450 genes (eg CYP4A2, etc). Off the cuff, I might think
about verfying that the 5' end of the mRNA is within this fragment, andm if
so, mapping the start site. The former can be done by Southern blot using
a 5' cDNA probe, and the latter can be done by S1 analysis, primer extension,
etc.
Benjamin
In <462jpd$iqn at server-b.cs.interbusiness.it>, Giorgio Spagnol <spagnol at galactica.it> writes:
>Dear fellow netters,
>I screened a genomic library by PCR with the intent to clone a gene
>promoter. The DNA segment I cloned does not contain a clear cut TATA box
>nor a CAAAT sequence.
>I guess I should consult a computer-based database to see if some
>consensus for transcription factor or DNA binding protein is present, in
>order to educately guess (or exclude) that the cloned DNA is indeed a
>regulatory gene segment and proceed with transfection trials.
>I'm new to this field, so any suggestion would be most welcome.
>I thank you anticipately.
>Giorgio
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